update workflow.cwl to include more recent pipeline outputs and refactors

mskcc / pluto-cwl

CWL workflows for helix filter scripts

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update workflow.cwl to include more recent pipeline outputs and refactors #69

Open stevekm opened 3 years ago

stevekm commented 3 years ago

The main workflow for pluto-cwl has been workflow_with_facets.cwl. This includes a number of updates besides just running facets including new pipeline outputs.

These updates need to be back-ported to workflow.cwl as well.